in the first Alien, the space jockey was found seated on the pilot's chair with a cavity in its chest. It just doesn't sync with Prometheus where it died in the escape pod instead. Or is it a different spaceship in Alien?

If I had to guess, I think the 'Engineers' have visited Earth more than once throughout the human history. Perhaps to observe and to teach civilization. To me, that's the best logic to explain why many extinct civilizations came to learn about the stellar map. We can only speculate to why the 'Engineers' then decide to annihilate Earth's population using the black goo, because the characters only came to that theory without any support from the 'Engineers' themselves. It doesn't necessarily be a weapon in fact as what we seen in the beginning of the movie. But if the annihilation theory is true, then its perhaps due to the human overpopulation, war and destruction of nature and Earth, that they choose to wipe the Earth clean and start all over again. (cue the Matrix - Architect agenda).

Your opinion over the symbolization of the four horsemen is probably a bit far fetched, but I can see where you get the relation from. Still, its probably a bit too heavy for the general viewers to comprehend.

Charlize Theron as Meredith Vickers is a tad dissapointing. I can't tell if she's an antagonist in the film. Idris Elba as Janek the captain had one line that aptly capture her characteristics in the movie.

Janek: Hey Vickers, Vickers.

Vickers: turns around...

Janek: I was wondering.....Are you a robot?

I love Charlize Theron. She just looks so cute in her scene, but the character just doesn't fit her that well. Being the corporate daughter of Peter Wayland, she had like a love-hate relationship with her father, but at the same time, she is this hard-stance, b*tch-cold boss in the Prometheus. In the end, she lost all that when Weyland emerges into the scene. Now she is this lonely, unwanted daughter who lost the respect of anyone and even lost control of the ship, and finally ends up a pancake on a distant moon pinned down under an alien spaceship for millenia. How depressing is that?

As for the timeline, Prometheus happened between 2089 - 2093 while Alien 1 happened in 2122. There is still the possibility that the sole alien queen in Prometheus hitched a ride in another alien spaceship and crash landed in LV-426 where Ellen Ripley first met the species. Most of us might be trying too hard to connect any relation between Prometheus to Alien 1 story arc, but its also plausible that both story just happen in the same universe without ever crossing path each other. Meaning to say that the queen alien from the 1979 installment came from a different origin entirely while the queen alien in Prometheus is a different breed.